Will run a refine job with -M ShortRunVoid this should take between 90 seconds and 400 seconds depending on machine speed refine output will follow and also be written to refine_test.log ############################################################################## # This software is licenced to : Global Phasing Ltd (hypatia) ############################################################################## ############################################################################## ## [refine] Framework for automatic refinement of macromolecules ############################################################################## Copyright (C) 1992-2012 by Global Phasing Limited All rights reserved. This software is proprietary to and embodies the confidential technology of Global Phasing Limited (GPhL). Possession, use, duplication or dissemination of the software is authorised only pursuant to a valid written licence from GPhL. Version: 1.11.5 <2012-11-28 00:41:41> ------------------------------------------------------------------------------ Authors: Bricogne G, Blanc E, Brandl M, Flensburg C, Keller P, Paciorek P, Roversi P, Sharff A, Smart O, Vonrhein C, Womack T (2012). BUSTER version 2.11.5. Cambridge, United Kingdom: Global Phasing Ltd. External: [TNT] B. Matthews, L. Ten Eyck, D. Tronrud (Univ. Oregon) Partial support by EU projects: VIZIER (LSHG-CT-2004-511960) SILVER (FP7-HEALTH-F3-2010-260644) Contact: buster-develop@GlobalPhasing.com ============================================================================== ################################ Basic checks ################################ NOTE : running with the following command line arguments: "-M ShortRunVoid -p sult1a3_tutorial_example_place_A3P.pdb -m 2a3r.mtz -autoncs -l A3P.grade_PDB_ligand.cif -d refine_test.dir" ######################### Checking PDB and MTZ file ########################## >>> pdbchk >>> >>> pdbchk >>> Extracted from file refine_test.dir/pdbchk.2.log : >>> pdbchk >>> >>> pdbchk >>> WARNING : 2 non-standard residues have 54 ATOM records >>> pdbchk >>> (when it should be HETATM) - see below >>> pdbchk >>> ATOM 1 P1 A3P A 500 57.230 104.904 -2.170 1.00 20.00 P >>> pdbchk >>> ATOM 2 O1P A3P A 500 56.097 105.339 -3.040 1.00 20.00 O >>> pdbchk >>> ATOM 3 O2P A3P A 500 58.511 104.618 -2.958 1.00 20.00 O >>> pdbchk >>> ATOM 4 O3P A3P A 500 56.896 103.668 -1.331 1.00 20.00 O >>> pdbchk >>> ATOM 5 P2 A3P A 500 56.749 111.663 1.111 1.00 20.00 P >>> pdbchk >>> ATOM 6 O4P A3P A 500 55.661 111.862 0.108 1.00 20.00 O >>> pdbchk >>> ATOM 7 O5P A3P A 500 56.232 111.639 2.552 1.00 20.00 O >>> pdbchk >>> ATOM 8 O6P A3P A 500 57.846 112.726 1.015 1.00 20.00 O >>> pdbchk >>> ATOM 9 O5' A3P A 500 57.489 110.242 0.883 1.00 20.00 O >>> pdbchk >>> ATOM 10 C5' A3P A 500 56.721 109.022 0.891 1.00 20.00 C >>> pdbchk >>> ... and 44 more occurences >>> pdbchk >>> >>> pdbchk >>> NOTE : changed 54 atoms in 2 residues from ATOM to HETATM - >>> pdbchk >>> see residues below: >>> pdbchk >>> NOTE : a check of the input PDB file (/home/osmart/2012/11/sult1a3_tutorial_example_place_A3P.pdb) initially gave some warning(s). We applied some changes to that PDB file and will be using the file refine_test.dir/pdbchk.pdb now. For details see above and refine_test.dir/pdbchk.2.log. NOTE : have removed 15 non-standard, initial REMARK records from input PDB file NOTE : using recorded X-ray weight from input PDB file (10.57) as starting value F/SIGF pairs : FP,SIGFP ############################################################################## # refining against FP,SIGFP with: FreeR_flag ############################################################################## NOTE : automatically selected B-factor refinement scheme "individual". It is possible to change this with the -B flag although this default is the recommended strategy. ################################ BIG cycle 1 ################################# NOTE : changed settings at start of BIG cycle 1: mxlcyc="20" TLSfixcycALL="1" running BUSTER in refine_test.dir/01-BUSTER/Cycle-1 [extra library /tmp/osmart-1354109042-refine__12987.elib]: NOTE : if the available wavelength (1.54180 A) is correct, a correction of the used formfactors might be useful ( P:0.2819 S:0.3173). This can be switched on automatically by setting the AutomaticFormfactorCorrection="yes" parameter on the command-line or explicitely with the FormfactorCorrection=":" parameter. You can set/change the wavelength on the command-line with: wavelength=. NOTE : setting solvent content to 0.496 NOTE : rms(bond) = 0.0098 A (details in refine_test.dir/01-BUSTER/Cycle-1/geometry.lis) running BUSTER-GELLY-TNT - see refine_test.dir/01-BUSTER/Cycle-1/LIST.html ... done NOTE : mean electron density of fragment (should be between 0.42-0.425 e/A^3): 0.420 NOTE : we're going to use the TNT sequence file refine_test.dir/01-BUSTER/Cycle-1/TNT.seq from now on NOTE : we're going to use the formfactor file refine_test.dir/01-BUSTER/Cycle-1/formfactor.dat from now on Ncyc Total Grms Rfact Rfree LLG Geom_Funct rmsBOND rmsANGLE 0 6.5391e+05 72.9300 0.212 0.247 0.000 5.6536e+04 0.010 1.050 1 6.5187e+05 116.4810 0.209 0.246 0.015 5.7611e+04 0.010 1.080 2 6.5124e+05 91.9071 0.208 0.246 0.017 5.7284e+04 0.010 1.060 3 6.5079e+05 64.3780 0.208 0.246 0.017 5.6819e+04 0.010 1.060 4 6.5021e+05 50.4295 0.208 0.246 0.018 5.6473e+04 0.010 1.050 5 6.4938e+05 94.2745 0.207 0.246 0.022 5.6588e+04 0.010 1.070 6 6.4859e+05 65.1387 0.206 0.245 0.027 5.6659e+04 0.010 1.060 7 6.4820e+05 79.4105 0.206 0.245 0.030 5.6900e+04 0.010 1.070 8 6.4794e+05 41.0313 0.205 0.245 0.030 5.6762e+04 0.010 1.060 9 6.4777e+05 38.7498 0.205 0.245 0.031 5.6647e+04 0.010 1.060 10 6.4739e+05 57.7063 0.205 0.245 0.032 5.6471e+04 0.010 1.060 11 6.4708e+05 84.8757 0.205 0.245 0.033 5.6469e+04 0.010 1.060 12 6.4679e+05 44.8222 0.204 0.245 0.034 5.6314e+04 0.010 1.050 13 6.4655e+05 28.0797 0.204 0.245 0.035 5.6249e+04 0.010 1.050 14 6.4644e+05 27.9731 0.204 0.245 0.035 5.6229e+04 0.010 1.050 15 6.4625e+05 47.5241 0.204 0.245 0.036 5.6248e+04 0.010 1.060 16 6.4615e+05 43.2545 0.204 0.245 0.037 5.6336e+04 0.010 1.060 17 6.4605e+05 21.0772 0.204 0.245 0.037 5.6219e+04 0.010 1.050 18 6.4596e+05 22.1101 0.204 0.245 0.037 5.6164e+04 0.010 1.050 19 6.4585e+05 25.8950 0.203 0.245 0.038 5.6158e+04 0.010 1.050 20 6.4567e+05 26.9351 0.203 0.245 0.039 5.6196e+04 0.010 1.060 -------------------------------------------------------- NOTE : created PDB file with 59 "atoms" to describe voids ################################ BIG cycle 2 ################################# NOTE : changed settings at start of BIG cycle 2: mxlcyc="1" running BUSTER in refine_test.dir/01-BUSTER/Cycle-2 [extra library refine_test.dir/01-BUSTER/my.geom]: NOTE : combining files for BABSLV NOTE : setting solvent content to 0.496 NOTE : rms(bond) = 0.0101 A (details in refine_test.dir/01-BUSTER/Cycle-2/geometry.lis) running BUSTER-GELLY-TNT - see refine_test.dir/01-BUSTER/Cycle-2/LIST.html ... done NOTE : mean electron density of fragment (should be between 0.42-0.425 e/A^3): 0.420 Ncyc Total Grms Rfact Rfree LLG Geom_Funct rmsBOND rmsANGLE 0 6.4334e+05 30.2193 0.200 0.241 0.000 5.6180e+04 0.010 1.060 1 6.4332e+05 21.6452 0.200 0.241 0.000 5.6165e+04 0.010 1.050 ======================================================================== best refinement in BUSTER-GELLY-TNT reached for FP,SIGFP with R/Rfree 0.2001/0.2414 for resolution range 24.85 - 2.62 A. refine_test.dir/01-BUSTER/Cycle-2/BUSTER.pdb refine_test.dir/01-BUSTER/Cycle-2/LIST.html refine_test.dir/01-BUSTER/Cycle-2/shell.01/mlphas.mtz ======================================================================== Additional files that might be of interest (use 'plotmtv' to visualise *.mtv files): refine_test.dir/R-Rfree_vs_cycle.mtv refine_test.dir/01-BUSTER/Cycle-2/shell.01/scales.txt refine_test.dir/01-BUSTER/Cycle-2/shell.01/R_Rfree.mtv refine_test.dir/01-BUSTER/Cycle-2/shell.01/wilson.mtv refine_test.dir/01-BUSTER/Cycle-2/shell.01/CCplots/cos_ccoef.001.mtv refine_test.dir/01-BUSTER/Cycle-2/shell.01/FOMs/cycle_003.mtv refine_test.dir/01-BUSTER/Cycle-2/shell.01/CCplots/R_Rfree.001.mtv NOTE : list of parameters set during this run = refine_test.dir/setvar.refine Normal termination (83 sec) ############################################################################## refine task has finished. Will now grep the final R/Rfree best refinement in BUSTER-GELLY-TNT reached for FP,SIGFP with R/Rfree 0.2001/0.2414 Please confirm that the R/Rfree value above is roughly 0.2001/0.2414 You can see the final model/map by running:f visualise-geometry-coot refine_test.dir If you have setup required external progams then test buster-report installation by: buster-report -d refine_test.dir Thanks for running the short test of 'refine'; see more about this test at http://www.globalphasing.com/buster/wiki/index.cgi?BusterShortRefineTest2